conda - smartpca stalling issue #70
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Never seen this problem. Your dataset is quite small and smartpca should
certainly complete in < 1 hour.
Please try the following:
Run with
numthreads: 1
shrinkmode: NO
and report back
Nick
…On Thu, Sep 2, 2021 at 10:11 AM William Marsh ***@***.***> wrote:
Hi,
I am having a few issues with running smartpca, which I have installed
using conda. The software initially runs successfully, but stalls after the
total number of snps killed in pass:xxxxx step.
Please find below the command line transcript in its entirety:
smartpca -p test.L.pca.par
parameter file: test.L.pca.par
THE INPUT PARAMETERS
PARAMETER NAME: VALUE
genotypename: test.geno
snpname: test.snp
indivname: test.ind
evecoutname: test.pca.evec
evaloutname: test.eval
lsqproject: YES
numoutevec: 4
numthreads: 8
smartpca version: 13050
norm used
lsqproject used
test.snp: genetic distance set from physical distance
nodata: 15:80297900
nodata: 19:27961945
number of samples used: 15 number of snps used: 299440
Using 8 threads, and partial sum lookup algorithm.
snp 1:1599161 ignored . allelecnt: 0 missing: 2
snp 1:1780878 ignored . allelecnt: 0 missing: 1
snp 1:1793071 ignored . allelecnt: 0 missing: 3
snp 1:1793786 ignored . allelecnt: 0 missing: 1
snp 1:2222583 ignored . allelecnt: 0 missing: 1
snp 1:2236697 ignored . allelecnt: 0 missing: 4
snp 1:3098715 ignored . allelecnt: 0 missing: 1
snp 1:3168280 ignored . allelecnt: 0 missing: 1
snp 1:3356405 ignored . allelecnt: 0 missing: 0
snp 1:3512516 ignored . allelecnt: 0 missing: 0
total number of snps killed in pass: 10948 used: 288492
I have attempted to run smartpca on a number of different datasets, of
differing sizes and origins, but the result/lack of result is the same. I
have left the program running for a number of weeks, but the command line
output does not differ after thirty minutes or so of running.
Is this a known issue? And if so how might I remedy?
Thanks,
William
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Hi Nick, Thanks for the rapid response. After an hour of running the above amendments, it has stalled in the same manner. William |
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Is it practical for you to share your dataset with me? I fear it will run
fine for me but we can try.
Else all I can suggest is that you run gdb and try and find out where it is
hanging
N
…On Thu, Sep 2, 2021 at 11:28 AM William Marsh ***@***.***> wrote:
Hi Nick,
Thanks for the rapid response. After an hour of running the above
amendments, it has stalled in the same manner.
William
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Hi Nick, I'll email you. William |
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Hi there, I encountered the same problem when running smartpca as described by William. Are there any solutions or suggestions for this issue? Thank you in advance! Serena |
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Hi,
I am having a few issues with running smartpca, which I have installed using conda. The software initially runs successfully, but stalls after the total number of snps killed in pass:xxxxx step.
Please find below the command line transcript in its entirety:
I have attempted to run smartpca on a number of different datasets, of differing sizes and origins, but the result/lack of result is the same. I have left the program running for a number of weeks, but the command line output does not differ after thirty minutes or so of running.
Is this a known issue? And if so how might I remedy?
Thanks,
William
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